closurizer 0.7.2__tar.gz → 0.8.0__tar.gz

{closurizer-0.7.2 → closurizer-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: closurizer
-Version: 0.7.2
+Version: 0.8.0
 Summary: Add closure expansion fields to kgx files following the Golr pattern
 Author: Kevin Schaper
 Author-email: kevin@tislab.org

{closurizer-0.7.2 → closurizer-0.8.0}/closurizer/cli.py

@@ -4,7 +4,8 @@ from closurizer.closurizer import add_closure
 
 
 @click.command()
-@click.option('--kg', required=True, help='KGX tar.gz archive')
+@click.option('--kg', required=False, help='KGX tar.gz archive to import (optional - if not provided, uses existing database)')
+@click.option('--database', required=False, default='monarch-kg.duckdb', help='Database path - if kg is provided, data will be loaded into this database; if kg is not provided, this database must already exist with nodes and edges tables (default: monarch-kg.duckdb)')
 @click.option('--closure', required=True, help='TSV file of closure triples')
 @click.option('--nodes-output', required=True, help='file write nodes kgx file with closure fields added')
 @click.option('--edges-output', required=True, help='file write edges kgx file with closure fields added')
@@ -14,8 +15,12 @@ from closurizer.closurizer import add_closure
 @click.option('--edge-fields-to-label', multiple=True, help='edge fields to with category, label, etc but not full closure exansion')
 @click.option('--node-fields', multiple=True, help='node fields to expand with closure IDs, labels, etc')
 @click.option('--grouping-fields', multiple=True, help='fields to populate a single value grouping_key field')
+@click.option('--multivalued-fields', multiple=True, help='fields containing pipe-delimited values to convert to varchar[] arrays in database')
 @click.option('--dry-run', is_flag=True, help='A dry run will not write the output file, but will print the SQL query')
+@click.option('--export-edges', is_flag=True, help='Export denormalized edges to TSV file (default: database only)')
+@click.option('--export-nodes', is_flag=True, help='Export denormalized nodes to TSV file (default: database only)')
 def main(kg: str,
+         database: str,
          closure: str,
          nodes_output: str,
          edges_output: str,
@@ -24,17 +29,25 @@ def main(kg: str,
          edge_fields: List[str] = None,
          edge_fields_to_label: List[str] = None,
          node_fields: List[str] = None,
-         grouping_fields: List[str] = None):
-    add_closure(kg_archive=kg,
-                closure_file=closure,
-                edge_fields=edge_fields,
-                edge_fields_to_label=edge_fields_to_label,
-                node_fields=node_fields,
-                edges_output_file=edges_output,
+         grouping_fields: List[str] = None,
+         multivalued_fields: List[str] = None,
+         export_edges: bool = False,
+         export_nodes: bool = False):
+    
+    add_closure(closure_file=closure,
                 nodes_output_file=nodes_output,
+                edges_output_file=edges_output,
+                kg_archive=kg,
+                database_path=database,
+                edge_fields=edge_fields or ['subject', 'object'],
+                edge_fields_to_label=edge_fields_to_label or [],
+                node_fields=node_fields or [],
                 additional_node_constraints=additional_node_constraints,
                 dry_run=dry_run,
-                grouping_fields=grouping_fields)
+                grouping_fields=grouping_fields or ['subject', 'negated', 'predicate', 'object'],
+                multivalued_fields=multivalued_fields or ['has_evidence', 'publications', 'in_taxon', 'in_taxon_label'],
+                export_edges=export_edges,
+                export_nodes=export_nodes)
 
 if __name__ == "__main__":
     main()

closurizer-0.8.0/closurizer/closurizer.py

@@ -0,0 +1,447 @@
+from typing import List, Optional
+
+import os
+import tarfile
+import duckdb
+
+def edge_columns(field: str, include_closure_fields: bool =True, node_column_names: list = None):
+    column_text = f"""
+       {field}.name as {field}_label, 
+       {field}.category as {field}_category,
+       {field}.namespace as {field}_namespace,       
+    """
+    if include_closure_fields:
+        column_text += f"""
+        {field}_closure.closure as {field}_closure,
+        {field}_closure_label.closure_label as {field}_closure_label,
+        """
+
+    # Only add taxon fields if they exist in the nodes table
+    if field in ['subject', 'object'] and node_column_names:
+        if 'in_taxon' in node_column_names:
+            column_text += f"""
+        {field}.in_taxon as {field}_taxon,"""
+        if 'in_taxon_label' in node_column_names:
+            column_text += f"""
+        {field}.in_taxon_label as {field}_taxon_label,"""
+        column_text += """
+        """
+    return column_text
+
+def edge_joins(field: str, include_closure_joins: bool =True, is_multivalued: bool = False):
+    if is_multivalued:
+        # For VARCHAR[] fields, use array containment with list_contains
+        join_condition = f"list_contains(edges.{field}, {field}.id)"
+    else:
+        # For VARCHAR fields, use direct equality
+        join_condition = f"edges.{field} = {field}.id"
+    
+    joins = f"""
+    left outer join nodes as {field} on {join_condition}"""
+    
+    if include_closure_joins:
+        joins += f"""
+    left outer join closure_id as {field}_closure on {field}.id = {field}_closure.id
+    left outer join closure_label as {field}_closure_label on {field}.id = {field}_closure_label.id"""
+    
+    return joins + "\n    "
+
+def evidence_sum(evidence_fields: List[str], edges_column_names: list = None):
+    """ Sum together the length of each field - assumes fields are VARCHAR[] arrays """
+    evidence_count_parts = []
+    for field in evidence_fields:
+        # Only include fields that actually exist in the edges table
+        if not edges_column_names or field in edges_column_names:
+            # All evidence fields are expected to be VARCHAR[] arrays
+            evidence_count_parts.append(f"ifnull(array_length({field}),0)")
+    
+    evidence_count_sum = "+".join(evidence_count_parts) if evidence_count_parts else "0"
+    return f"{evidence_count_sum} as evidence_count,"
+
+
+def node_columns(predicate):
+    # strip the biolink predicate, if necessary to get the field name
+    field = predicate.replace('biolink:','')
+
+    return f"""
+    case when count(distinct {field}_edges.object) > 0 then array_agg(distinct {field}_edges.object) else null end as {field},
+    case when count(distinct {field}_edges.object_label) > 0 then array_agg(distinct {field}_edges.object_label) else null end as {field}_label,
+    count (distinct {field}_edges.object) as {field}_count,
+    case when count({field}_closure.closure) > 0 then list_distinct(flatten(array_agg({field}_closure.closure))) else null end as {field}_closure,
+    case when count({field}_closure_label.closure_label) > 0 then list_distinct(flatten(array_agg({field}_closure_label.closure_label))) else null end as {field}_closure_label,
+    """
+
+def node_joins(predicate):
+    # strip the biolink predicate, if necessary to get the field name
+    field = predicate.replace('biolink:','')
+    return f"""
+      left outer join denormalized_edges as {field}_edges 
+        on nodes.id = {field}_edges.subject 
+           and {field}_edges.predicate = 'biolink:{field}'
+      left outer join closure_id as {field}_closure
+        on {field}_edges.object = {field}_closure.id
+      left outer join closure_label as {field}_closure_label
+        on {field}_edges.object = {field}_closure_label.id
+    """
+
+
+def grouping_key(grouping_fields, edges_column_names: list = None):
+    if not grouping_fields:
+        return "null as grouping_key"
+    fragments = []
+    for field in grouping_fields:
+        # Only include fields that actually exist in the edges table
+        if not edges_column_names or field in edges_column_names:
+            if field == 'negated':
+                fragments.append(f"coalesce(cast({field} as varchar).replace('true','NOT'), '')")
+            else:
+                fragments.append(field)
+    if not fragments:
+        return "null as grouping_key"
+    grouping_key_fragments = ", ".join(fragments)
+    return f"concat_ws('|', {grouping_key_fragments}) as grouping_key"
+
+
+
+
+def load_from_archive(kg_archive: str, db, multivalued_fields: List[str]):
+    """Load nodes and edges tables from tar.gz archive"""
+    
+    tar = tarfile.open(f"{kg_archive}")
+
+    print("Loading node table...")
+    node_file_name = [member.name for member in tar.getmembers() if member.name.endswith('_nodes.tsv') ][0]
+    tar.extract(node_file_name,)
+    node_file = f"{node_file_name}"
+    print(f"node_file: {node_file}")
+
+    db.sql(f"""
+    create or replace table nodes as select *,  substr(id, 1, instr(id,':') -1) as namespace from read_csv('{node_file_name}', header=True, sep='\t', AUTO_DETECT=TRUE)
+    """)
+
+    edge_file_name = [member.name for member in tar.getmembers() if member.name.endswith('_edges.tsv') ][0]
+    tar.extract(edge_file_name)
+    edge_file = f"{edge_file_name}"
+    print(f"edge_file: {edge_file}")
+
+    db.sql(f"""
+    create or replace table edges as select * from read_csv('{edge_file_name}', header=True, sep='\t', AUTO_DETECT=TRUE)
+    """)
+    
+    # Convert multivalued fields to arrays
+    prepare_multivalued_fields(db, multivalued_fields)
+    
+    # Clean up extracted files
+    if os.path.exists(f"{node_file}"):
+        os.remove(f"{node_file}")
+    if os.path.exists(f"{edge_file}"):
+        os.remove(f"{edge_file}")
+
+
+def prepare_multivalued_fields(db, multivalued_fields: List[str]):
+    """Convert specified fields to varchar[] arrays in both nodes and edges tables"""
+    
+    # Convert multivalued fields in nodes table to varchar[] arrays
+    nodes_table_info = db.sql("DESCRIBE nodes").fetchall()
+    node_column_names = [col[0] for col in nodes_table_info]
+    node_column_types = {col[0]: col[1] for col in nodes_table_info}
+    
+    for field in multivalued_fields:
+        if field in node_column_names:
+            # Check if field is already VARCHAR[] - if so, skip conversion
+            if 'VARCHAR[]' in node_column_types[field].upper():
+                print(f"Field '{field}' in nodes table is already VARCHAR[], skipping conversion")
+                continue
+                
+            print(f"Converting field '{field}' in nodes table to VARCHAR[]")
+            # Create a new column with proper array type and replace the original
+            db.sql(f"""
+            alter table nodes add column {field}_array VARCHAR[]
+            """)
+            db.sql(f"""
+            update nodes set {field}_array = 
+                case 
+                    when {field} is null or {field} = '' then null
+                    else split({field}, '|')
+                end
+            """)
+            db.sql(f"""
+            alter table nodes drop column {field}
+            """)
+            db.sql(f"""
+            alter table nodes rename column {field}_array to {field}
+            """)
+
+    # Convert multivalued fields in edges table to varchar[] arrays
+    edges_table_info = db.sql("DESCRIBE edges").fetchall()
+    edge_column_names = [col[0] for col in edges_table_info]
+    edge_column_types = {col[0]: col[1] for col in edges_table_info}
+    
+    for field in multivalued_fields:
+        if field in edge_column_names:
+            # Check if field is already VARCHAR[] - if so, skip conversion
+            if 'VARCHAR[]' in edge_column_types[field].upper():
+                print(f"Field '{field}' in edges table is already VARCHAR[], skipping conversion")
+                continue
+                
+            print(f"Converting field '{field}' in edges table to VARCHAR[]")
+            # Create a new column with proper array type and replace the original
+            db.sql(f"""
+            alter table edges add column {field}_array VARCHAR[]
+            """)
+            db.sql(f"""
+            update edges set {field}_array = 
+                case 
+                    when {field} is null or {field} = '' then null
+                    else split({field}, '|')
+                end
+            """)
+            db.sql(f"""
+            alter table edges drop column {field}
+            """)
+            db.sql(f"""
+            alter table edges rename column {field}_array to {field}
+            """)
+
+
+def add_closure(closure_file: str,
+                nodes_output_file: str,
+                edges_output_file: str,
+                kg_archive: Optional[str] = None,
+                database_path: str = 'monarch-kg.duckdb',
+                node_fields: List[str] = [],
+                edge_fields: List[str] = ['subject', 'object'],
+                edge_fields_to_label: List[str] = [],
+                additional_node_constraints: Optional[str] = None,
+                dry_run: bool  = False,
+                evidence_fields: List[str] = ['has_evidence', 'publications'],
+                grouping_fields: List[str] = ['subject', 'negated', 'predicate', 'object'],
+                multivalued_fields: List[str] = ['has_evidence', 'publications', 'in_taxon', 'in_taxon_label'],
+                export_edges: bool = False,
+                export_nodes: bool = False
+                ):
+    # Validate input parameters
+    if not kg_archive and not os.path.exists(database_path):
+        raise ValueError("Either kg_archive must be specified or database_path must exist")
+    
+    print("Generating closure KG...")
+    if kg_archive:
+        print(f"kg_archive: {kg_archive}")
+    print(f"database_path: {database_path}")
+    print(f"closure_file: {closure_file}")
+
+    # Connect to database
+    db = duckdb.connect(database=database_path)
+
+    if not dry_run:
+        print(f"fields: {','.join(edge_fields)}")
+        print(f"output_file: {edges_output_file}")
+
+        # Load data based on input method
+        if kg_archive:
+            load_from_archive(kg_archive, db, multivalued_fields)
+        else:
+            # Database already exists and contains data
+            # Check if namespace column exists, add it if needed
+            node_column_names = [col[0] for col in db.sql("DESCRIBE nodes").fetchall()]
+            if 'namespace' not in node_column_names:
+                print("Adding namespace column to nodes table...")
+                db.sql("ALTER TABLE nodes ADD COLUMN namespace VARCHAR")
+                db.sql("UPDATE nodes SET namespace = substr(id, 1, instr(id,':') -1)")
+            
+            # Convert multivalued fields to arrays
+            prepare_multivalued_fields(db, multivalued_fields)
+
+        # Load the relation graph tsv in long format mapping a node to each of it's ancestors
+        db.sql(f"""
+        create or replace table closure as select * from read_csv('{closure_file}', sep='\t', names=['subject_id', 'predicate_id', 'object_id'], AUTO_DETECT=TRUE)
+        """)
+
+        db.sql("""
+        create or replace table closure_id as select subject_id as id, array_agg(object_id) as closure from closure group by subject_id
+        """)
+
+        db.sql("""
+        create or replace table closure_label as select subject_id as id, array_agg(name) as closure_label from closure join nodes on object_id = id
+        group by subject_id
+        """)
+
+        db.sql("""
+        create or replace table descendants_id as 
+        select object_id as id, array_agg(subject_id) as descendants 
+        from closure 
+        group by object_id
+        """)
+
+        db.sql("""
+        create or replace table descendants_label as 
+        select object_id as id, array_agg(name) as descendants_label 
+        from closure 
+        join nodes on subject_id = nodes.id
+        group by object_id
+        """)
+
+    # Get edges table schema to determine which fields are VARCHAR[]
+    edges_table_info = db.sql("DESCRIBE edges").fetchall()
+    edges_table_types = {col[0]: col[1] for col in edges_table_info}
+    edges_column_names = [col[0] for col in edges_table_info]
+    
+    # Get nodes table schema to check for available columns
+    nodes_table_info = db.sql("DESCRIBE nodes").fetchall()
+    node_column_names = [col[0] for col in nodes_table_info]
+    
+    # Build edge joins with proper multivalued field handling
+    edge_field_joins = []
+    for field in edge_fields:
+        is_multivalued = field in multivalued_fields and 'VARCHAR[]' in edges_table_types.get(field, '').upper()
+        edge_field_joins.append(edge_joins(field, is_multivalued=is_multivalued))
+    
+    edge_field_to_label_joins = []
+    for field in edge_fields_to_label:
+        is_multivalued = field in multivalued_fields and 'VARCHAR[]' in edges_table_types.get(field, '').upper()
+        edge_field_to_label_joins.append(edge_joins(field, include_closure_joins=False, is_multivalued=is_multivalued))
+    
+    edges_query = f"""
+    create or replace table denormalized_edges as
+    select edges.*, 
+           {"".join([edge_columns(field, node_column_names=node_column_names) for field in edge_fields])}
+           {"".join([edge_columns(field, include_closure_fields=False, node_column_names=node_column_names) for field in edge_fields_to_label])} 
+           {evidence_sum(evidence_fields, edges_column_names)}
+           {grouping_key(grouping_fields, edges_column_names)}  
+    from edges
+        {"".join(edge_field_joins)}
+        {"".join(edge_field_to_label_joins)}
+    """
+
+    print(edges_query)
+
+    additional_node_constraints = f"where {additional_node_constraints}" if additional_node_constraints else ""
+    
+    # Get nodes table info to handle multivalued fields in the query
+    nodes_table_info = db.sql("DESCRIBE nodes").fetchall()
+    nodes_table_column_names = [col[0] for col in nodes_table_info]
+    nodes_table_types = {col[0]: col[1] for col in nodes_table_info}
+    
+    # Create field selections for nodes, converting VARCHAR[] back to pipe-delimited strings
+    nodes_field_selections = []
+    for field in nodes_table_column_names:
+        if field in multivalued_fields and 'VARCHAR[]' in nodes_table_types[field].upper():
+            # Convert VARCHAR[] back to pipe-delimited string
+            nodes_field_selections.append(f"list_aggregate({field}, 'string_agg', '|') as {field}")
+        else:
+            # Regular field, use as-is (but need to specify for GROUP BY)
+            nodes_field_selections.append(f"nodes.{field}")
+    
+    nodes_base_fields = ",\n        ".join(nodes_field_selections)
+    
+    nodes_query = f"""        
+    create or replace table denormalized_nodes as
+    select {nodes_base_fields}, 
+        {"".join([node_columns(node_field) for node_field in node_fields])}
+    from nodes
+        {node_joins('has_phenotype')}
+    {additional_node_constraints}
+    group by {", ".join([f"nodes.{field}" for field in nodes_table_column_names])}
+    """
+    print(nodes_query)
+
+
+    if not dry_run:
+
+        db.sql(edges_query)
+
+        # Export edges to TSV only if requested
+        if export_edges:
+            edge_closure_replacements = [
+                f"""
+                list_aggregate({field}_closure, 'string_agg', '|') as {field}_closure,
+                list_aggregate({field}_closure_label, 'string_agg', '|') as {field}_closure_label
+                """
+                for field in edge_fields
+            ]
+            
+            # Add conversions for original multivalued fields back to pipe-delimited strings
+            edge_table_info = db.sql("DESCRIBE denormalized_edges").fetchall()
+            edge_table_column_names = [col[0] for col in edge_table_info]
+            edge_table_types = {col[0]: col[1] for col in edge_table_info}
+            
+            # Create set of closure fields already handled by edge_closure_replacements
+            closure_fields_handled = set()
+            for field in edge_fields:
+                closure_fields_handled.add(f"{field}_closure")
+                closure_fields_handled.add(f"{field}_closure_label")
+            
+            multivalued_replacements = [
+                f"list_aggregate({field}, 'string_agg', '|') as {field}"
+                for field in multivalued_fields 
+                if field in edge_table_column_names and 'VARCHAR[]' in edge_table_types[field].upper()
+                and field not in closure_fields_handled
+            ]
+            
+            all_replacements = edge_closure_replacements + multivalued_replacements
+            edge_closure_replacements = "REPLACE (\n" + ",\n".join(all_replacements) + ")\n"
+
+            edges_export_query = f"""
+            -- write denormalized_edges as tsv
+            copy (select * {edge_closure_replacements} from denormalized_edges) to '{edges_output_file}' (header, delimiter '\t')
+            """
+            print(edges_export_query)
+            db.sql(edges_export_query)
+
+        db.sql(nodes_query)
+        
+        # Add descendant columns separately to avoid memory issues with large GROUP BY
+        print("Adding descendant columns to denormalized_nodes...")
+        db.sql("alter table denormalized_nodes add column has_descendant VARCHAR[]")
+        db.sql("alter table denormalized_nodes add column has_descendant_label VARCHAR[]") 
+        db.sql("alter table denormalized_nodes add column has_descendant_count INTEGER")
+        
+        db.sql("""
+        update denormalized_nodes 
+        set has_descendant = descendants_id.descendants
+        from descendants_id 
+        where denormalized_nodes.id = descendants_id.id
+        """)
+        
+        db.sql("""
+        update denormalized_nodes 
+        set has_descendant_label = descendants_label.descendants_label
+        from descendants_label 
+        where denormalized_nodes.id = descendants_label.id
+        """)
+        
+        db.sql("""
+        update denormalized_nodes 
+        set has_descendant_count = coalesce(array_length(has_descendant), 0)
+        """)
+        
+        # Export nodes to TSV only if requested
+        if export_nodes:
+            # Get denormalized_nodes table info to handle array fields in export
+            denorm_nodes_table_info = db.sql("DESCRIBE denormalized_nodes").fetchall()
+            denorm_nodes_column_names = [col[0] for col in denorm_nodes_table_info]
+            denorm_nodes_types = {col[0]: col[1] for col in denorm_nodes_table_info}
+            
+            # Find all VARCHAR[] fields that need conversion to pipe-delimited strings
+            array_field_replacements = [
+                f"list_aggregate({field}, 'string_agg', '|') as {field}"
+                for field in denorm_nodes_column_names 
+                if 'VARCHAR[]' in denorm_nodes_types[field].upper()
+            ]
+            
+            # The descendants fields are already handled by the general VARCHAR[] logic above
+            # No need to add them separately
+            
+            if array_field_replacements:
+                nodes_replacements = "REPLACE (\n" + ",\n".join(array_field_replacements) + ")\n"
+                nodes_export_query = f"""
+                -- write denormalized_nodes as tsv
+                copy (select * {nodes_replacements} from denormalized_nodes) to '{nodes_output_file}' (header, delimiter '\t')
+                """
+            else:
+                nodes_export_query = f"""
+                -- write denormalized_nodes as tsv
+                copy (select * from denormalized_nodes) to '{nodes_output_file}' (header, delimiter '\t')
+                """
+            print(nodes_export_query)
+            db.sql(nodes_export_query)

{closurizer-0.7.2 → closurizer-0.8.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "closurizer"
-version = "0.7.2"
+version = "0.8.0"
 description = "Add closure expansion fields to kgx files following the Golr pattern"
 authors = ["Kevin Schaper <kevin@tislab.org>"]
 

closurizer-0.7.2/closurizer/closurizer.py

@@ -1,191 +0,0 @@
-from typing import List, Optional
-
-import os
-import tarfile
-import duckdb
-
-def edge_columns(field: str, include_closure_fields: bool =True):
-    column_text = f"""
-       {field}.name as {field}_label, 
-       {field}.category as {field}_category,
-       {field}.namespace as {field}_namespace,       
-    """
-    if include_closure_fields:
-        column_text += f"""
-        {field}_closure.closure as {field}_closure,
-        {field}_closure_label.closure_label as {field}_closure_label,
-        """
-
-    if field in ['subject', 'object']:
-        column_text += f"""
-        {field}.in_taxon as {field}_taxon,
-        {field}.in_taxon_label as {field}_taxon_label,
-        """
-    return column_text
-
-def edge_joins(field: str, include_closure_joins: bool =True):
-    return f"""
-    left outer join nodes as {field} on edges.{field} = {field}.id
-    left outer join closure_id as {field}_closure on {field}.id = {field}_closure.id
-    left outer join closure_label as {field}_closure_label on {field}.id = {field}_closure_label.id
-    """
-
-def evidence_sum(evidence_fields: List[str]):
-    """ Sum together the length of each field after splitting on | """
-    evidence_count_sum = "+".join([f"ifnull(len(split({field}, '|')),0)" for field in evidence_fields])
-    return f"{evidence_count_sum} as evidence_count,"
-
-
-def node_columns(predicate):
-    # strip the biolink predicate, if necessary to get the field name
-    field = predicate.replace('biolink:','')
-
-    return f"""
-    string_agg({field}_edges.object, '|') as {field},
-    string_agg({field}_edges.object_label, '|') as {field}_label,
-    count (distinct {field}_edges.object) as {field}_count,
-    list_aggregate(list_distinct(flatten(array_agg({field}_closure.closure))), 'string_agg', '|') as {field}_closure,
-    list_aggregate(list_distinct(flatten(array_agg({field}_closure_label.closure_label))), 'string_agg', '|') as {field}_closure_label,
-    """
-
-def node_joins(predicate):
-    # strip the biolink predicate, if necessary to get the field name
-    field = predicate.replace('biolink:','')
-    return f"""
-      left outer join denormalized_edges as {field}_edges 
-        on nodes.id = {field}_edges.subject 
-           and {field}_edges.predicate = 'biolink:{field}'
-      left outer join closure_id as {field}_closure
-        on {field}_edges.object = {field}_closure.id
-      left outer join closure_label as {field}_closure_label
-        on {field}_edges.object = {field}_closure_label.id
-    """
-
-
-def grouping_key(grouping_fields):
-    fragments = []
-    for field in grouping_fields:
-        if field == 'negated':
-            fragments.append(f"coalesce(cast({field} as varchar).replace('true','NOT'), '')")
-        else:
-            fragments.append(field)
-    grouping_key_fragments = ", ".join(fragments)
-    return f"concat_ws('|', {grouping_key_fragments}) as grouping_key"
-
-
-def add_closure(kg_archive: str,
-                closure_file: str,
-                nodes_output_file: str,
-                edges_output_file: str,
-                node_fields: List[str] = [],
-                edge_fields: List[str] = ['subject', 'object'],
-                edge_fields_to_label: List[str] = [],
-                additional_node_constraints: Optional[str] = None,
-                dry_run: bool  = False,
-                evidence_fields: List[str] = ['has_evidence', 'publications'],
-                grouping_fields: List[str] = ['subject', 'negated', 'predicate', 'object']
-                ):
-    print("Generating closure KG...")
-    print(f"kg_archive: {kg_archive}")
-    print(f"closure_file: {closure_file}")
-
-    db = duckdb.connect(database='monarch-kg.duckdb')
-
-    if not dry_run:
-        print(f"fields: {','.join(edge_fields)}")
-        print(f"output_file: {edges_output_file}")
-
-        tar = tarfile.open(f"{kg_archive}")
-
-        print("Loading node table...")
-        node_file_name = [member.name for member in tar.getmembers() if member.name.endswith('_nodes.tsv') ][0]
-        tar.extract(node_file_name,)
-        node_file = f"{node_file_name}"
-        print(f"node_file: {node_file}")
-
-        db.sql(f"""
-        create or replace table nodes as select *,  substr(id, 1, instr(id,':') -1) as namespace from read_csv('{node_file_name}', header=True, sep='\t', AUTO_DETECT=TRUE)
-        """)
-
-        edge_file_name = [member.name for member in tar.getmembers() if member.name.endswith('_edges.tsv') ][0]
-        tar.extract(edge_file_name)
-        edge_file = f"{edge_file_name}"
-        print(f"edge_file: {edge_file}")
-
-        db.sql(f"""
-        create or replace table edges as select * from read_csv('{edge_file_name}', header=True, sep='\t', AUTO_DETECT=TRUE)
-        """)
-
-        # Load the relation graph tsv in long format mapping a node to each of it's ancestors
-        db.sql(f"""
-        create or replace table closure as select * from read_csv('{closure_file}', sep='\t', names=['subject_id', 'predicate_id', 'object_id'], AUTO_DETECT=TRUE)
-        """)
-
-        db.sql("""
-        create or replace table closure_id as select subject_id as id, array_agg(object_id) as closure from closure group by subject_id
-        """)
-
-        db.sql("""
-        create or replace table closure_label as select subject_id as id, array_agg(name) as closure_label from closure join nodes on object_id = id
-        group by subject_id
-        """)
-
-    edges_query = f"""
-    create or replace table denormalized_edges as
-    select edges.*, 
-           {"".join([edge_columns(field) for field in edge_fields])}
-           {"".join([edge_columns(field, include_closure_fields=False) for field in edge_fields_to_label])} 
-           {evidence_sum(evidence_fields)}
-           {grouping_key(grouping_fields)}  
-    from edges
-        {"".join([edge_joins(field) for field in edge_fields])}
-        {"".join([edge_joins(field, include_closure_joins=False) for field in edge_fields_to_label])}
-    """
-
-    print(edges_query)
-
-    additional_node_constraints = f"where {additional_node_constraints}" if additional_node_constraints else ""
-    nodes_query = f"""        
-    create or replace table denormalized_nodes as
-    select nodes.*, 
-        {"".join([node_columns(node_field) for node_field in node_fields])}
-    from nodes
-        {node_joins('has_phenotype')}
-    {additional_node_constraints}
-    group by nodes.*
-    """
-    print(nodes_query)
-
-
-    if not dry_run:
-
-
-        edge_closure_replacements = [
-            f"""
-            list_aggregate({field}_closure, 'string_agg', '|') as {field}_closure,
-            list_aggregate({field}_closure_label, 'string_agg', '|') as {field}_closure_label
-            """
-            for field in edge_fields
-        ]
-
-        edge_closure_replacements = "REPLACE (\n" + ",\n".join(edge_closure_replacements) + ")\n"
-
-        edges_export_query = f"""
-        -- write denormalized_edges as tsv
-        copy (select * {edge_closure_replacements} from denormalized_edges) to '{edges_output_file}' (header, delimiter '\t')
-        """
-        print(edges_export_query)
-        db.query(edges_export_query)
-
-        nodes_export_query = f"""
-        -- write denormalized_nodes as tsv
-        copy (select * from denormalized_nodes) to '{nodes_output_file}' (header, delimiter '\t')
-        """
-        print(nodes_export_query)
-
-
-        # Clean up extracted node & edge files
-        if os.path.exists(f"{node_file}"):
-            os.remove(f"{node_file}")
-        if os.path.exists(f"{edge_file}"):
-            os.remove(f"{edge_file}")